Claims
- 1. A method for the structure-based design of a drug that can act as an inhibitor of at least two different biological entities, said method comprising the steps of:
(a) providing at least one structure of a wild type target protein or an inhibitor-wild type target protein complex; (b) providing at least one structure of a variant target protein or an inhibitor-variant target protein complex; (c) comparing at least one structure from step (a) with at least one structure from step (b) to determine whether there exists a common three-dimensionally conserved substructure comprising the atomic coordinates of the structurally conserved atoms of the inhibitors and structurally conserved atoms of the target proteins; and (d) if a conserved substructure exists, using said atomic coordinates of said conserved substructure to select a compound having atoms matching those of said structurally conserved atoms of the inhibitors, wherein the selection of said compound is performed using computer modeling.
- 2. A method for the structure-based drug design of a broad spectrum inhibitor, said method comprising the steps of:
(a) providing at least one structure of a wild type target protein or an inhibitor-wild type target protein complex; (b) providing at least one structure of a variant target protein or an inhibitor-variant target protein complex; (c) comparing at least one structure from step (a) with at least one structure from step (b) to determine whether there exists a common three-dimensionally conserved substructure comprising the atomic coordinates of the structurally conserved atoms the target proteins or a common three-dimensionally conserved substructure comprising the atomic coordinates of the structurally conserved atoms of the inhibitors and structurally conserved atoms of the target proteins; and (d) if a conserved substructure exists, using said atomic coordinates of said conserved substructure to select a compound having atoms matching those of said structurally conserved atoms of the inhibitors or to design a compound that binds to said target protein, wherein the selection of said compound is performed using computer modeling.
- 3. The method of claim 1, further comprising the steps of:
(e) comparing at least one structure from step (a) with at least one structure from step (b) to determine whether there exists a three-dimensionally non-conserved substructure comprising the atomic coordinates of the structurally non-conserved atoms of the inhibitors and structurally non-conserved atoms of the target proteins; and (f) if a non-conserved substructure exists, using said atomic coordinates of said non-conserved substructure to reject a compound having atoms matching those of said structurally non-conserved atoms of the inhibitors, wherein the rejection of said compound is performed in conjunction with computer modeling.
- 4. The method of claim 1, wherein at least two structures from step b are used in step c.
- 5. The method of claim 4, wherein at least four structures from step b are used in step c.
- 6. The method of claim 4, wherein said target proteins comprise at least two variant forms.
- 7. The method of claim 6, wherein said target proteins comprise at least four variant forms
- 8. The method of claim 1, wherein the inhibitors in said inhibitor-wild type target protein complex and said inhibitor-variant target protein complex are the same.
- 9. The method of claim 1, wherein the inhibitors in said inhibitor-wild type target protein complex and said inhibitor-variant target protein complex are different.
- 10. The method of claim 1, wherein said inhibitors are competitive inhibitors.
- 11. The method of claim 1, wherein said inhibitors are noncompetitive inhibitors.
- 12. The method of claim 1, wherein said inhibitors are reversible inhibitors.
- 13. The method of claim 1, wherein said inhibitors are irreversible inhibitors.
- 14. The method of claim 1, wherein said variant target protein is a homologous target protein.
- 15. The method of claim 1, wherein said variant target protein is a mutant target protein.
- 16. The method of claim 1, wherein at least one of said structures is a crystal structure.
- 17. The method of claim 1, wherein at least one of said structures is an nmr structure.
- 18. The method of claim 1, wherein at least one of said structures is derived using computational methods.
- 19. The method of claim 1, wherein said target protein is expressed in a microbe and said microbe is selected from the group consisting of viruses, bacteria, protozoa, or fungi.
- 20. The method of claim 1, wherein said target protein is expressed in a neoplasm.
- 21. The method of claims 19 or 20, wherein said target protein is selected from the group consisting of an enzyme, a receptor, a structural protein, a component of a macromolecular complex, a component of a metabolic pathway, or an assembly of biological molecules.
- 22. The method of claim 21, wherein said enzyme is selected from the group consisting of reverse transcriptases, proteases, DNA and RNA polymerases, methylases, oxidases, hydratases, esterases, acyl transferases, helicases, topoisomerases, and kinases.
- 23. The method of claim 22, wherein said enzyme is HIV protease.
- 24. The method of claim 23, wherein said inhibitors are selected from the group consisting of indinavir, nelfinavir, ritonavir, saquinavir, amprenavir, lopinavir, and UIC-94003.
- 25. The method of claim 23, wherein said structurally conserved atoms of the inhibitor and structurally conserved atoms of the protease have the atomic structural coordinates as provided in Table 8.
- 26. The method of claim 22, wherein said enzyme is 3-dehydroquinate dehydratase.
- 27. The method of claim 26, wherein said structurally conserved atoms of the 3-dehydroquinate dehydratase have the atomic structural coordinates as provided in Table 12.
- 28. A compound having a chemical structure selected using the method of claim 19, wherein said compound has broad spectrum activity against wild type and variant microbes.
- 29. A compound having a chemical structure selected using the method of claim 20, wherein said compound has broad spectrum activity against wild type and variant neoplasms.
- 30. The compound of claims 28 or 29, wherein said compound has an IC50, variant/IC50, wild type ratio of less than 20.
- 31. The compound of claim 30, wherein said IC50, variant/IC50, wildtype ratio is less than 6.
- 32. The compound of claims 28 or 29, wherein said compound has broad spectrum activity against at least 3 mutant biological entities.
- 33. The compound of claim 28, wherein said compound has broad spectrum activity against at least 3 different organisms expressing homologous target proteins.
- 34. A pharmaceutical composition comprising a compound of claim 28 and a pharmaceutically acceptable carrier or diluent.
- 35. A pharmaceutical composition comprising a compound of claim 29 and a pharmaceutically acceptable carrier or diluent.
- 36. A compound having a chemical structure selected using the method of any one of claims 23-25, wherein said compound has broad spectrum activity against HIV protease.
- 37. The compound of claim 36, wherein said compound has an IC50, variant/IC50, wild type ratio of less than 10.
- 38. The compound of claim 37, wherein said IC50, variant/IC50, wild type ratio is less than 6.
- 39. The compound of claim 36, wherein said compound has broad spectrum activity against at least 3 mutant biological entities.
- 40. A pharmaceutical composition comprising a compound of claim 36 and a pharmaceutically acceptable carrier or diluent.
- 41. A compound having a chemical structure selected using the method of claims 26 or 27, wherein said compound has broad spectrum activity against 3-dehydroquinate dehydratase.
- 42. The compound of claim 41, wherein said compound has an IC50, variant/IC50, wild type ratio of less than 20.
- 43. The compound of claim 42, wherein said IC50, variant/IC50, wild type ratio is less than 10.
- 44. The compound of claim 43, wherein said compound has broad spectrum activity against at least 3 mutant biological entities.
- 45. The compound of claim 41, wherein said compound has broad spectrum activity against at least 3 different organisms expressing homologous target proteins.
- 46. A pharmaceutical composition comprising a compound of claim 41 and a pharmaceutically acceptable carrier or diluent.
- 47. A method of treating a microbial infection in a patient, said method comprising the step of administering to said patient a pharmaceutical composition of claim 34 in an amount effective to prevent or treat said infection.
- 48. A method of treating a neoplasm in a patient in need thereof, said method comprising the step of administering to said patient a pharmaceutical composition of claim 35 in amounts effective to treat said neoplasm.
- 49. A method of treating an HIV infection in a patient in need thereof, said method comprising the step of administering to said patient a pharmaceutical composition of claim 40 in amounts effective to treat said infection.
- 50. A method of treating a bacterial infection in a patient in need thereof, said method comprising the step of administering to said patient a pharmaceutical composition of claim 46 in amounts effective to treat said infection.
- 51. The method of claim 50, wherein said bacterial infection is caused by a bacterium selected from the group consisting of C jejuni, V. cholerae, Y pestis, B. anthracis, P. putidas, and M. tuberculosis.
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] The application claims benefit of U.S. Provisional Application No. 0/344,788, filed Jan. 7, 2002, and No. 60/383,575, filed May 29, 2002, each of which is hereby incorporated by reference.
Provisional Applications (2)
|
Number |
Date |
Country |
|
60344788 |
Jan 2002 |
US |
|
60383575 |
May 2002 |
US |